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java.lang.Objectorg.jmol.smiles.SmilesGenerator
public class SmilesGenerator
Double bond, allene, square planar and tetrahedral stereochemistry only not octahedral or trigonal bipyramidal. No attempt at canonicalization -- unnecessary for model searching. see SmilesMatcher and package.html for details Bob Hanson, Jmol 12.0.RC17 2010.06.5
Field Summary | |
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private int |
atomCount
|
private JmolNode[] |
atoms
|
private java.util.BitSet |
bsAromatic
|
private java.util.BitSet |
bsBondsDn
|
private java.util.BitSet |
bsBondsUp
|
private java.util.BitSet |
bsIncludingH
|
private java.util.BitSet |
bsSelected
|
private java.util.BitSet |
bsToDo
|
private java.util.Hashtable |
htRings
|
private java.util.Hashtable |
htRingsSequence
|
private int |
nPairs
|
private JmolNode |
prevAtom
|
private JmolNode[] |
prevSp2Atoms
|
private java.lang.StringBuffer |
ringSets
|
private SmilesSearch.VTemp |
vTemp
|
Constructor Summary | |
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SmilesGenerator()
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Method Summary | |
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private void |
addBracketedBioName(java.lang.StringBuffer sb,
JmolNode a,
java.lang.String atomName)
|
private java.lang.String |
addStereoCheck(int atomIndex,
JmolNode[] stereo,
int i,
java.lang.String s)
checks a group and either adds a new group to the growing check string or returns null |
private java.lang.String |
checkStereoPairs(JmolNode atom,
int atomIndex,
JmolNode[] stereo,
int stereoFlag)
|
private void |
dumpRingKeys(java.lang.StringBuffer sb,
java.util.Hashtable ht)
|
(package private) java.lang.String |
getBioSmiles(JmolNode[] atoms,
int atomCount,
java.util.BitSet bsSelected,
boolean allowUnmatchedRings,
boolean addCrossLinks,
java.lang.String comment)
|
private char |
getBondStereochemistry(JmolEdge bond,
JmolNode atomFrom)
Retrieves the saved character based on the index of the bond. |
private java.lang.String |
getRingCache(int i0,
int i1,
java.util.Hashtable ht)
|
protected static java.lang.String |
getRingKey(int i0,
int i1)
|
(package private) java.lang.String |
getSmiles(JmolNode[] atoms,
int atomCount,
java.util.BitSet bsSelected)
|
private JmolNode |
getSmiles(java.lang.StringBuffer sb,
JmolNode atom,
boolean allowConnectionsToOutsideWorld,
boolean allowBranches)
|
private java.lang.String |
getSmilesComponent(JmolNode atom,
java.util.BitSet bs,
boolean allowConnectionsToOutsideWorld)
creates a valid SMILES string from a model. |
private static java.lang.String |
getStereoFlag(JmolNode atom0,
JmolNode[] atoms,
int nAtoms,
SmilesSearch.VTemp v)
|
private void |
setBondDirections()
Creates global BitSets bsBondsUp and bsBondsDown. |
private java.lang.String |
sortInorganic(JmolNode atom,
java.util.List v)
We must sort the bond vector such that a diaxial pair is first and last. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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private JmolNode[] atoms
private int atomCount
private java.util.BitSet bsSelected
private java.util.BitSet bsAromatic
private java.lang.StringBuffer ringSets
private SmilesSearch.VTemp vTemp
private int nPairs
private java.util.BitSet bsBondsUp
private java.util.BitSet bsBondsDn
private java.util.BitSet bsToDo
private JmolNode prevAtom
private JmolNode[] prevSp2Atoms
private java.util.Hashtable htRingsSequence
private java.util.Hashtable htRings
private java.util.BitSet bsIncludingH
Constructor Detail |
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public SmilesGenerator()
Method Detail |
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java.lang.String getSmiles(JmolNode[] atoms, int atomCount, java.util.BitSet bsSelected) throws InvalidSmilesException
InvalidSmilesException
java.lang.String getBioSmiles(JmolNode[] atoms, int atomCount, java.util.BitSet bsSelected, boolean allowUnmatchedRings, boolean addCrossLinks, java.lang.String comment) throws InvalidSmilesException
InvalidSmilesException
private void addBracketedBioName(java.lang.StringBuffer sb, JmolNode a, java.lang.String atomName)
private java.lang.String getSmilesComponent(JmolNode atom, java.util.BitSet bs, boolean allowConnectionsToOutsideWorld) throws InvalidSmilesException
atom
- bs
- allowConnectionsToOutsideWorld
-
InvalidSmilesException
private char getBondStereochemistry(JmolEdge bond, JmolNode atomFrom)
bond
- atomFrom
-
private void setBondDirections()
private JmolNode getSmiles(java.lang.StringBuffer sb, JmolNode atom, boolean allowConnectionsToOutsideWorld, boolean allowBranches)
private java.lang.String sortInorganic(JmolNode atom, java.util.List v)
atom
- v
-
private java.lang.String checkStereoPairs(JmolNode atom, int atomIndex, JmolNode[] stereo, int stereoFlag)
private static java.lang.String getStereoFlag(JmolNode atom0, JmolNode[] atoms, int nAtoms, SmilesSearch.VTemp v)
atom0
- atoms
- nAtoms
- v
-
private java.lang.String addStereoCheck(int atomIndex, JmolNode[] stereo, int i, java.lang.String s)
atomIndex
- stereo
- i
- s
-
private java.lang.String getRingCache(int i0, int i1, java.util.Hashtable ht)
private void dumpRingKeys(java.lang.StringBuffer sb, java.util.Hashtable ht)
protected static java.lang.String getRingKey(int i0, int i1)
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